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AB SCIEX TripleTOF® 5600/5600+ InstrumentsSystem User GuideDocument Number: D5033331 ARelease Date: May 2012

Safety and Regulatory InformationAB SCIEX TripleTOF® 5600/5600+ Instruments10 of 116System User Guide D5033331 ARegulatory ComplianceThis system comp

DuoSpray™ Ion Source User ReferenceAB SCIEX TripleTOF® 5600/5600+ Instruments100 of 116System User Guide D5033331 AFigure 7-6 Corona discharge needle

DuoSpray™ Ion Source User ReferenceSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 101 of 1165. Install the ion source. Refer t

DuoSpray™ Ion Source User ReferenceAB SCIEX TripleTOF® 5600/5600+ Instruments102 of 116System User Guide D5033331 AConsumablesThe following tables li

System User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ System 103 of 1168Cleaning and MaintenanceRegularly clean and maintain the instrument for op

Cleaning and MaintenanceAB SCIEX TripleTOF® 5600/5600+ Instruments104 of 116System User Guide D5033331 A• Avoid ignition sources when working with fl

Cleaning and MaintenanceSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 105 of 1163. Unscrew the cap and dispose of the waste.4

Cleaning and MaintenanceAB SCIEX TripleTOF® 5600/5600+ Instruments106 of 116System User Guide D5033331 AThis section provides instructions for perfor

Cleaning and MaintenanceSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 107 of 116• Prepare and store all organic solutions and

Cleaning and MaintenanceAB SCIEX TripleTOF® 5600/5600+ Instruments108 of 116System User Guide D5033331 AClean the Curtain PlateCaution: Potential Ins

Cleaning and MaintenanceSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 109 of 1166. Inspect the curtain plate for solvent stai

Safety and Regulatory InformationSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 11 of 116International• Electromagnetic Compat

Cleaning and MaintenanceAB SCIEX TripleTOF® 5600/5600+ Instruments110 of 116System User Guide D5033331 A

System User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 111 of 1169Basic System TroubleshootingThis appendix contains basic information

Basic System TroubleshootingAB SCIEX TripleTOF® 5600/5600+ Instruments112 of 116System User Guide D5033331 A

System User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 113 of 116ARecommended Calibration IonsThe following tables list the standards r

Recommended Calibration IonsAB SCIEX TripleTOF® 5600/5600+ Instruments114 of 116System User Guide D5033331 ATable A-5 APCI Negative Calibration Solut

System User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 115 of 116BExact Masses and Chemical FormulasPPGTable B-1 contains the exact mon

Exact Masses and Chemical FormulasAB SCIEX TripleTOF® 5600/5600+ Instruments116 of 116System User Guide D5033331 AReserpine (C33H40N2O9) Taurocholic

Safety and Regulatory InformationAB SCIEX TripleTOF® 5600/5600+ Instruments12 of 116System User Guide D5033331 ADo not dispose of equipment as unsort

Safety and Regulatory InformationSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 13 of 116Occupational Health and Safety Symbol

Safety and Regulatory InformationAB SCIEX TripleTOF® 5600/5600+ Instruments14 of 116System User Guide D5033331 AMains SupplyThe mass spectrometer pow

Safety and Regulatory InformationSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 15 of 116Protective Earth ConductorThe mains s

Safety and Regulatory InformationAB SCIEX TripleTOF® 5600/5600+ Instruments16 of 116System User Guide D5033331 AInstrument Disposal (Waste Electrical

System User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 17 of 1161System InformationThe AB SCIEX TripleTOF® 5600/5600+ system is designe

System InformationAB SCIEX TripleTOF® 5600/5600+ Instruments18 of 116System User Guide D5033331 ASystem OverviewFigure 1-1 to Figure 1-2 show the mas

System InformationSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 19 of 1168 Serial (RS-232) cable connection for the syringe p

AB SCIEX71 Four Valley Dr., Concord, Ontario, Canada. L4K 4V8.AB Sciex LP is ISO 9001 registered.© 2012 AB SCIEX.Printed in Canada.This document is pr

System InformationAB SCIEX TripleTOF® 5600/5600+ Instruments20 of 116System User Guide D5033331 ADress Panel LEDsStart Up the SystemBefore the system

System InformationSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 21 of 116Use the following procedures if you need to turn on

System InformationAB SCIEX TripleTOF® 5600/5600+ Instruments22 of 116System User Guide D5033331 AUse the Integrated Syringe PumpEdit the Hardware Pro

System InformationSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 23 of 1165. Click Configure Pump.Figure 1-4 Harvard Syringe d

System InformationAB SCIEX TripleTOF® 5600/5600+ Instruments24 of 116System User Guide D5033331 A2. Adjust the post, shown in Figure 1-6, so that it

System InformationSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 25 of 1163. Turn the side screws as shown in Figure 1-7 to se

System InformationAB SCIEX TripleTOF® 5600/5600+ Instruments26 of 116System User Guide D5033331 AReset the Syringe PumpIf the Analyst TF software sto

System User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 27 of 1162Hardware Profiles and ProjectsSample Workflows• Instrument Setup on pa

Hardware Profiles and ProjectsAB SCIEX TripleTOF® 5600/5600+ Instruments28 of 116System User Guide D5033331 A2 Create an acquisition method.Basic Acq

Hardware Profiles and ProjectsSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 29 of 116Hardware ProfilesA hardware profile tell

System User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 3 of 116ContentsSafety and Regulatory Information . . . . . . . . . . . . . . .

Hardware Profiles and ProjectsAB SCIEX TripleTOF® 5600/5600+ Instruments30 of 116System User Guide D5033331 A3. In the Profile Name field (Figure 2-2

Hardware Profiles and ProjectsSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 31 of 1164. Click Add Device.In the Available Dev

Hardware Profiles and ProjectsAB SCIEX TripleTOF® 5600/5600+ Instruments32 of 116System User Guide D5033331 A9. (Optional) If using an integrated syr

Hardware Profiles and ProjectsSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 33 of 116Add Peripheral Devices to Hardware Profi

Hardware Profiles and ProjectsAB SCIEX TripleTOF® 5600/5600+ Instruments34 of 116System User Guide D5033331 A• If the device uses Ethernet communicat

Hardware Profiles and ProjectsSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 35 of 116Create Projects and SubprojectsTo use a

Hardware Profiles and ProjectsAB SCIEX TripleTOF® 5600/5600+ Instruments36 of 116System User Guide D5033331 ACreate a New SubprojectSubprojects can o

Hardware Profiles and ProjectsSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 37 of 116Switch Between Projects and Subprojects•

Hardware Profiles and ProjectsAB SCIEX TripleTOF® 5600/5600+ Instruments38 of 116System User Guide D5033331 ABack up the API Instrument ProjectBack u

System User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 39 of 1163Instrument Tuning and Calibrating Run the Verify Performance Only opti

ContentsAB SCIEX TripleTOF® 5600/5600+ Instruments4 of 116System User Guide D5033331 AChapter 3 Instrument Tuning and Calibrating. . . . . . . . . .

Instrument Tuning and CalibratingAB SCIEX TripleTOF® 5600/5600+ Instruments40 of 116System User Guide D5033331 A4. Select a tuning solution. Make sur

System User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 41 of 1164Basic Acquisition MethodsAn acquisition method consists of the method

Basic Acquisition MethodsAB SCIEX TripleTOF® 5600/5600+ Instruments42 of 116System User Guide D5033331 A10. Next steps: The newly created acquisition

Basic Acquisition MethodsSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 43 of 116Add an Experiment1. Right-click the period wh

Basic Acquisition MethodsAB SCIEX TripleTOF® 5600/5600+ Instruments44 of 116System User Guide D5033331 AScan TechniquesThe system is a versatile and

Basic Acquisition MethodsSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 45 of 116Product Ion Mass SpectrometryIn a product ion

Basic Acquisition MethodsAB SCIEX TripleTOF® 5600/5600+ Instruments46 of 116System User Guide D5033331 AFigure 4-1 Ion optics path and parametersItem

Basic Acquisition MethodsSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 47 of 1161 IonSpray Voltage Floating (ISVF)Source and

Basic Acquisition MethodsAB SCIEX TripleTOF® 5600/5600+ Instruments48 of 116System User Guide D5033331 A1DP (Declustering Potential)Compound The DP p

Basic Acquisition MethodsSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 49 of 116Acquisition Method Editor Icons3 Ion Release

ContentsSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 5 of 116Show a Spectrum from a TIC . . . . . . . . . . . . . . . . .

Basic Acquisition MethodsAB SCIEX TripleTOF® 5600/5600+ Instruments50 of 116System User Guide D5033331 ASyringe Pump Opens the Syringe Pump Propertie

System User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 51 of 1165BatchesA batch is a collection of information about the samples to be

BatchesAB SCIEX TripleTOF® 5600/5600+ Instruments52 of 116System User Guide D5033331 AFigure 5-1 Queue Options dialog3. In the Max Num Waiting Sample

BatchesSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 53 of 116Add Sets and Samples to a BatchA set can consist of a single sa

BatchesAB SCIEX TripleTOF® 5600/5600+ Instruments54 of 116System User Guide D5033331 AFor example, if 3 is typed, the sample names would be samplenam

BatchesSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 55 of 1162. In the Calibrate Every _ Samples field, type the number of s

BatchesAB SCIEX TripleTOF® 5600/5600+ Instruments56 of 116System User Guide D5033331 A2. Click View > Sample Queue.The Queue Manager opens with al

BatchesSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 57 of 116Select Vial Positions using the Locations Tab (Optional)1. In t

BatchesAB SCIEX TripleTOF® 5600/5600+ Instruments58 of 116System User Guide D5033331 ABatch and Acquisition Method Editor TipsBatch Editor Right-Clic

BatchesSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 59 of 116Queue States and Device StatusThe Queue Manager shows queue, ba

ContentsAB SCIEX TripleTOF® 5600/5600+ Instruments6 of 116System User Guide D5033331 AChapter 9 Basic System Troubleshooting. . . . . . . . . . . . .

BatchesAB SCIEX TripleTOF® 5600/5600+ Instruments60 of 116System User Guide D5033331 AView Instrument and Device Status IconsIcons representing the i

BatchesSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 61 of 116Table 5-3 Instrument and Device Status (showing the instrument

BatchesAB SCIEX TripleTOF® 5600/5600+ Instruments62 of 116System User Guide D5033331 AQueue Right-Click MenuRight-click in the Queue table to access

BatchesSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 63 of 116Stop Sample Stops the sample in the queue.Abort Sample Aborts a

BatchesAB SCIEX TripleTOF® 5600/5600+ Instruments64 of 116System User Guide D5033331 A

System User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 65 of 1166Analyzing and Processing DataUse the sample files installed in the Exa

Analyzing and Processing DataAB SCIEX TripleTOF® 5600/5600+ Instruments66 of 116System User Guide D5033331 A4. To skip to the next sample in the data

Analyzing and Processing DataSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 67 of 116Show Experimental Data in Tables • With a

Analyzing and Processing DataAB SCIEX TripleTOF® 5600/5600+ Instruments68 of 116System User Guide D5033331 A3. Click Explore > Show > Show ADC

Analyzing and Processing DataSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 69 of 116Show TICs from a SpectrumPrerequisite: Th

System User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 7 of 116Safety and Regulatory InformationThis section contains general safety-re

Analyzing and Processing DataAB SCIEX TripleTOF® 5600/5600+ Instruments70 of 116System User Guide D5033331 AThere are several methods for extracting

Analyzing and Processing DataSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 71 of 116To generate an XIC using the maximum peak

Analyzing and Processing DataAB SCIEX TripleTOF® 5600/5600+ Instruments72 of 116System User Guide D5033331 A2. Click Explore > Extract Ions > U

Analyzing and Processing DataSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 73 of 1162. Click Explore > Show > Show Base

Analyzing and Processing DataAB SCIEX TripleTOF® 5600/5600+ Instruments74 of 116System User Guide D5033331 AGenerate XWCsThe user can extract up to t

Analyzing and Processing DataSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 75 of 116The TWC opens in a pane below the DAD spe

Analyzing and Processing DataAB SCIEX TripleTOF® 5600/5600+ Instruments76 of 116System User Guide D5033331 ASave Explore History The Explore History

Analyzing and Processing DataSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 77 of 116Data ProcessingGraphical data can be proc

Analyzing and Processing DataAB SCIEX TripleTOF® 5600/5600+ Instruments78 of 116System User Guide D5033331 AMove a pane • Select the graph. Click Win

Analyzing and Processing DataSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 79 of 116Zoom in on the y-axis1. Position the poin

Safety and Regulatory InformationAB SCIEX TripleTOF® 5600/5600+ Instruments8 of 116System User Guide D5033331 ACaution: A caution indicates an operat

Analyzing and Processing DataAB SCIEX TripleTOF® 5600/5600+ Instruments80 of 116System User Guide D5033331 AShow Base Peak ChromatogramGenerates a BP

Analyzing and Processing DataSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 81 of 116Show History View a summary of data proce

Analyzing and Processing DataAB SCIEX TripleTOF® 5600/5600+ Instruments82 of 116System User Guide D5033331 A

System User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 83 of 1167DuoSpray™ Ion Source User ReferenceThe DuoSpray™ ion source combines a

DuoSpray™ Ion Source User ReferenceAB SCIEX TripleTOF® 5600/5600+ Instruments84 of 116System User Guide D5033331 AProbesChoose the probe and method m

DuoSpray™ Ion Source User ReferenceSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 85 of 116APCI ProbeThe APCI probe is suitabl

DuoSpray™ Ion Source User ReferenceAB SCIEX TripleTOF® 5600/5600+ Instruments86 of 116System User Guide D5033331 AGas and Electrical ConnectionsGas a

DuoSpray™ Ion Source User ReferenceSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 87 of 116A pressure switch mounted on the so

DuoSpray™ Ion Source User ReferenceAB SCIEX TripleTOF® 5600/5600+ Instruments88 of 116System User Guide D5033331 A1. Adjust the black electrode adjus

DuoSpray™ Ion Source User ReferenceSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 89 of 1162. Install the sample tubing nut on

Safety and Regulatory InformationSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 9 of 116Shipping Crate Labels and IndicatorsTa

DuoSpray™ Ion Source User ReferenceAB SCIEX TripleTOF® 5600/5600+ Instruments90 of 116System User Guide D5033331 AOptimize the TurboIonSpray Probe Op

DuoSpray™ Ion Source User ReferenceSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 91 of 116For LC pumps, use a value between 3

DuoSpray™ Ion Source User ReferenceAB SCIEX TripleTOF® 5600/5600+ Instruments92 of 116System User Guide D5033331 Aespecially if the probe is too low,

DuoSpray™ Ion Source User ReferenceSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 93 of 116Caution: Potential Equipment Damage

DuoSpray™ Ion Source User ReferenceAB SCIEX TripleTOF® 5600/5600+ Instruments94 of 116System User Guide D5033331 AAdjust the Corona Discharge NeedleW

DuoSpray™ Ion Source User ReferenceSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 95 of 116Optimize the APCI Probe Temperature

DuoSpray™ Ion Source User ReferenceAB SCIEX TripleTOF® 5600/5600+ Instruments96 of 116System User Guide D5033331 A1. Switch to a mobile phase that is

DuoSpray™ Ion Source User ReferenceSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 97 of 116Clean the Electrode TubeClean the e

DuoSpray™ Ion Source User ReferenceAB SCIEX TripleTOF® 5600/5600+ Instruments98 of 116System User Guide D5033331 A6. Remove the electrode tube from t

DuoSpray™ Ion Source User ReferenceSystem User GuideD5033331 AAB SCIEX TripleTOF® 5600/5600+ Instruments 99 of 116Remove the Corona Discharge NeedleT